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作者： Francesca Grisoni Gisbert Schneider

Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: ***/ETHmodlab/scaffold_hopping_whales . less

关键词： Virtual Screening Scaffold Hopping High-throughput Screening programming language Chemoinformatics Drug Natural product Weighted Holistic Atom Localization and Entity Shape (WHALES)

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Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators

Transcriptional Activation of Heterochromatin by Recruitment...

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作者： Lukas Frank Robin Weinmann Fabian Erdel Jorge Trojanowski Karsten Rippe

The transition from silenced heterochromatin to a biologically active state and vice versa is a fundamental part of the implementation of cell type-specific gene expression programs. To reveal structure–function relationships and dissect the underlying mechanisms, experiments that ectopically induce transcription are highly informative. In particular, the approach to perturb chromatin states by recruiting fusions of the catalytically inactive dCas9 protein in a sequence-specific manner to a locus of interest has been used in numerous applications. Here, we describe how this approach can be applied to activate pericentric heterochromatin (PCH) in mouse cells as a prototypic silenced state by providing protocols for the following workflow: (a) Recruitment of dCas9 fusion constructs with the strong transcriptional activator VPR to PCH. (b) Analysis of the resulting changes in chromatin compaction, epigenetic marks, and active transcription by fluorescence microscopy-based readouts. (c) Automated analysis of the resulting images with a set of scripts in the R programming language. Furthermore, we discuss how parameters for chromatin decondensation and active transcription are extracted from these experiments and can be combined with other readouts to gain insights into PCH activation. less

关键词： CRISPR Fluorescence Microscopy Transfection Immunostaining Fiji Cell And Tissue Culture Image Analysis ImageJ Microscopy programming language Mus musculus Oryctolagus cuniculus Capra hircus Image quantification dCas9 Decondensation Chromocenter Pericentric heterochromatin Anti-rabbit anti-H3K27Ac

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Mathematical Linear programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer

Mathematical Linear Programming to Model MicroRNAs-Mediated ...

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作者： Vijaykumar Yogesh Muley

Genes are transcribed into various RNA molecules, and a portion of them called messenger RNA (mRNA) is then translated into proteins in the process known as gene expression. Gene expression is a high-energy demanding process, and aberrant expression changes often manifest into pathophysiology. Therefore, gene expression is tightly regulated by several factors at different levels. MicroRNAs (miRNAs) are one of the powerful post-transcriptional regulators involved in key biological processes and diseases. They inhibit the translation of their mRNA targets or degrade them in a sequence-specific manner, and hence control the rate of protein synthesis. In recent years, in response to experimental limitations, several computational methods have been proposed to predict miRNA target genes based on sequence complementarity and structural features. However, these predictions yield a large number of false positives. Integration of gene and miRNA expression data drastically alleviates this problem. Here, I describe a mathematical linear modeling approach to identify miRNA targets at the genome scale using gene and miRNA expression data. Mathematical modeling is faster and more scalable to genome-level compared to conventional statistical modeling approaches. less

关键词： RNA Interference Mathematical Modeling Statistical Modeling Gene Expression Profiling Python programming language Gene expression Gene regulation miRNA MicroRNA Post-transcriptional gene regulation Linear programming Linear modeling Gurobi Mathematical optimization

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FPGA-based implementation of bistable function blocks defined in the IEC 61131

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MICROPROCESSORS AND MICROSYSTEMS 2019年 65卷 37-46页

作者： Chmiel, M. Silesian Tech Univ Inst Elect Akad Str 16 PL-44100 Gliwice Poland

This article discusses the possibilities of using FPGAs in order to construct fast PLCs that execute serial-cyclic program control loop. The PLCs bistable function blocks of the IEC 61131-3 standard with particular emphasis on the possible FPGA implementations are presented. The FPGA hardware support is implemented in such a way that it does not interfere with the normal, serial-cyclic program execution. It enables a significant reduction in the timing of the result execution after loading new input data in the memory cells. Moreover, such an implementation of bistable function blocks allows for seamless use in any programming language. Both the IL text language and the graphical languages (LD and FBD) can freely use the advantages of such a solution. (C) 2018 Elsevier B.V. All rights reserved.

关键词： Programmable logic controllers (PLC) IEC 61131 programming language Field programmable gate arrays (FPGA) Bistable function blocks

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Interfering Peptides Targeting Protein–Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence

Interfering Peptides Targeting Protein–Protein Interactions...

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作者： Alexander Hofmann Alexander Minges Georg Groth

Interfering peptides (iPs) have been recognized as valuable substances to specifically target protein–protein interactions (PPIs) in senescence and disease. Although the concept of iPs has been validated for several PPIs in medical and pharmaceutical research, little attention so far has been paid to the enormous potential iPs that may provide to target and control plant growth and developmental processes or plant environmental responses. However, recent research on PPIs in the ethylene signaling pathway has identified the synthetic peptide NOP-1 derived from the nuclear localization signal of ethylene regulator EIN2 as an efficient inhibitor of typical ethylene responses such as ripening, aging, and senescence. Biophysical and biochemical studies on purified recombinant proteins of the ethylene receptor family from various plant species demonstrate that the synthetic peptide binds in the nM-μM range at the plant target. Here, we describe methods to evaluate and quantify the effect of the NOP-1 peptide on flower senescence as a typical ethylene response in the intact plant system. This approach will help to systematically advance our technological capability to delay plant ethylene responses and to expand shelf-life or vase life of fruits and flowers. less

关键词： Spectroscopy HPLC Python Data analysis programming language Rubus idaeus Protein–protein interactions Interfering peptides Ethylene signaling Plant senescence

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Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach

Methods to Identify and Study the Evolution of Pseudogenes U...

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作者： Jacques Dainat Pierre Pontarotti

The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described. less

关键词： Phylogenetic Tree Analysis Genome Assembly Genome Annotation Ensembl programming language Speciation Phylogeny Paralogy Pseudogene Orthology

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An Accelerated Java programming Summer Program --- Poster Abstract

Journal of Computing Sciences in Colleges

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Journal of Computing Sciences in Colleges 2024年第8期39卷

作者： Ching-yu Huang Paolien Wang Department of Computer Science & Technology Kean University Union

Since 2018, New Jersey high schools have been required to offer computer science courses, and the nature of these courses can vary significantly. This proposal suggests implementing an accelerated Java summer program specifically designed for incoming new students at colleges. The freshman class has expanded to include many students with no coding background, and some have a limited background but are either unwilling or unable to take the AP Computer Science exam. Consequently, these students often enroll in a full semester CS1 course as their first programming course at college. However, an accelerated Java summer program would better serve some students, building upon their existing knowledge. This program allows freshman students to advance to the second programming class in their first semester, instead of being mixed with other students with no coding background. This proposed program represents a departure from the conventional 4-credit Java section, compressing what is typically a 15-week course (4 hours per week, comprising 3 hours of lecture and 1 hour of lab) into an intensive 2-week format. The success of this program depends on the invited students' prior programming experience, motivation, and their ability to quickly grasp the curriculum, allowing them to thrive in a fast-paced learning environment. The development of a cohort community of students through this shared experience is expected to positively impact student retention and success.

关键词： AP CS1 Java accelerated programming language summer program

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A compiler and virtual machine for constraint-logic object-oriented programming with Muli

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JOURNAL OF COMPUTER languageS 2019年 53卷 63-78页

作者： Dagefoerde, Jan C. Kuchen, Herbert Univ Munster ERCIS Leonardo Campus 3 D-48149 Munster Germany

The development of enterprise software typically relies on object-oriented (OO) programming languages. However, OO languages are not particularly suited for the implementation of software which involves solving complicated search problems with dynamically appearing constraints, e. g. as found in logistics. Aiming to improve this situation, we propose the Munster Logic-imperative language (Muli). As a constraint-logic OO language, it facilitates an integrated implementation of applications that use aspects from both constraint-logic and object-oriented programming, thus eliminating the need to resort to JNI for the integration of search applications that are written in a (constraint) logic language. Muli extends Java by logic variables and encapsulated search. Its runtime is based on a symbolic Java virtual machine and leverages constraint solvers. Outside of search regions, Muli behaves just like Java. We motivate the benefits of integrating object-oriented programming and constraint-logic programming into a single language and introduce novel concepts that are required for a seamless integration. Furthermore, we present an operational semantics and transfer concepts and semantics into implementations of a compiler and a virtual machine.

关键词： programming paradigm integration programming language Constraint-logic programming Operational semantics Virtual machine implementation

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Type Capabilities for Object-Oriented programming languages 20th

Type Capabilities for Object-Oriented Programming Languages

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20th International Conference on Formal Engineering Methods (ICFEM)

作者： Wu, Xi Lu, Yi Meiring, Patrick A. Hayes, Ian J. Meinicke, Larissa A. Univ Queensland Sch ITEE Brisbane Qld 4072 Australia Oracle Labs Brisbane Qld 4000 Australia

ISBN: (纸本)9783030024505;9783030024499

Capabilities are used to control access to system resources. In modern programming languages that execute code with different levels of trust in the same process, the propagation of such capabilities must be controlled so that they cannot unintentionally be obtained by unauthorised code. In this paper, we present a statically-checked type system for object-oriented programming languages which guarantees that capabilities are restricted to authorised code. Capabilities are regarded as types that are granted to code based on a user-defined policy file (similar to that used by Java). In order to provide a finer-grained access control, the type system supports parameterised capabilities to more precisely identify system resources. The approach is illustrated using file-access examples.

关键词： Capability-based security Access control Authorisation Parameterisation programming language

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Assembly language and assembler for deep learning accelerators

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High Technology Letters 2019年第4期25卷 386-394页

作者： Lan Huiying Wu Linyang Han Dong Du Zidong Intelligent Processor Research Center Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190P.R.China University of Chinese Academy of Sciences Beijing 100049P.R.China Cambricon Technologies Corporation Limited Beijing 100191P.R.China

Deep learning accelerators(DLAs)have been proved to be efficient computational devices for processing deep learning *** DLA architectures are proposed and applied to different applications and ***,for most DLAs,their programming interfaces are either difficult to use or not efficient *** DLAs require programmers to directly write instructions,which is time-consuming and *** prevailing programming interface for DLAs is high-performance libraries and deep learning frameworks,which are easy to be used and very friendly to users,but their high abstraction level limits their control capacity over the hardware resources thus compromises the efficiency of the accelerator.A design of the programming interface is for *** various existing DLAs and their programming methods are analyzed and a methodology for designing programming interface for DLAs is proposed,which is a high-level assembly language(called DLA-AL),assembler and runtime for ***-AL is composed of a low-level assembly language and a set of high-level *** allows experienced experts to fully exploit the potential of DLAs and achieve near-optimal ***,by using DLA-AL,end-users who have little knowledge of the hardware are able to develop deep learning algorithms on DLAs spending minimal programming efforts.

关键词： deep learning deep learning accelerator(DLA) assembly language programming language

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